We have a bioinformatic resource that largely replaces the functionality of this project! See our new repository here: https://github.com/nanoporetech/pychopper

This repository is now unsupported and we do not recommend its use. Please contact Oxford Nanopore: support@nanoporetech.com for help with your application if it is not possible to upgrade to our new resources, or we are missing key features.

Utility pipeline for running pychopper, a tool to identify full length cDNA reads

This simple Snakemake pipeline is running pychopper (a tool to identify full length cDNA reads) on a directory containing fastq files. Check out the pychopper repository for more information on these parameters, here.

Getting Started

Input

The input files and parameters are specified in config.yml:

• fastq_dir - directory with the fastq files. The pipeline will concatenate them into a single input fastq file.
• primers - the cDNA primers as a fasta snippet.
• aln_params - pychopper alignment parameters.
• target_length - number of bases to scan at each end.
• sample_size - number of random samples when calculating score cutoff.
• score_percentile - score cutoff percentile.
• heu_mode - use heuristic mode if true.
• heu_stringency - stringency in heuristic mode.

Output

• output/full_length_reads.fastq - stranded full length reads.
• output/unclassified_reads.fastq- unclassified reads.
• output/pychopper_report.pdf - report PDF.
• output/stats.tsv - classification statistics.
• output/alignment_scores.tsv - alignment scores.
• input/reads.fastq - concatenated input reads.
• input/primers.fas - input cDNA primers.
• versions.txt - installed software versions.

Dependencies

• miniconda - install it according to the instructions.
• snakemake install using conda.
• The rest of the dependencies are automatically installed using the conda feature of snakemake.

Layout

• README.md
• Snakefile - master snakefile
• config.yml - YAML configuration file
• snakelib/ - snakefiles collection included by the master snakefile
• lib/ - python files included by analysis scripts and snakefiles
• scripts/ - analysis scripts

Installation

Clone the repository:

git clone https://github.com/nanoporetech/pipeline-pychopper

Usage:

Edit config.yml to set the input datasets and parameters then issue:

snakemake --use-conda -j <num_cores> all

Help

Licence and Copyright

(c) 2019 Oxford Nanopore Technologies Ltd.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

FAQs and tips

References and Supporting Information

Research Release

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.